Question

Did anyone successfully install apgl graph library for python? http://packages.python.org/apgl/ Is there other alternative graph libraries in python that does the same stuff as apgl with the same simplicity?

Currently i’m using Ubuntu 12.04 distro and i’ve installed the dependent libraries here:

sudo apt-get install pip
sudo pip install numpy
sudo apt-get install libatlas-base-dev gfortran g++
sudo pip install scipy
sudo pip install matplotlib
sudo pip install agpl

It installed successfully,then when i did:

>>> import apgl
>>> apgl.test()

I encounter the error:

>>> apgl.test()
Running tests from /usr/local/lib/python2.7/dist-packages/apgl
..............s....................................................E...........E.................................................ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss.....................................................................E.........E.........................................sssssssss...sssssss..sssssssssssssssssssssssssssss.................................s....s..ss..........
======================================================================
ERROR: testLoad (graph.test.SparseGraphTest.SparseGraphTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/apgl/graph/test/MatrixGraphTest.py", line 1619, in testLoad
    graph.save(tempFile)
  File "/usr/local/lib/python2.7/dist-packages/apgl/graph/AbstractMatrixGraph.py", line 558, in save
    import zipfile
  File "/usr/lib/python2.7/zipfile.py", line 464, in <module>
    class ZipExtFile(io.BufferedIOBase):
AttributeError: 'module' object has no attribute 'BufferedIOBase'

======================================================================
ERROR: testPickle (graph.test.SparseGraphTest.SparseGraphTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/apgl/graph/test/MatrixGraphTest.py", line 2309, in testPickle
    output = pickle.dumps(graph)
  File "/usr/lib/python2.7/pickle.py", line 1374, in dumps
    Pickler(file, protocol).dump(obj)
  File "/usr/lib/python2.7/pickle.py", line 224, in dump
    self.save(obj)
  File "/usr/lib/python2.7/pickle.py", line 306, in save
    rv = reduce(self.proto)
  File "/usr/lib/python2.7/copy_reg.py", line 84, in _reduce_ex
    dict = getstate()
  File "/usr/local/lib/python2.7/dist-packages/apgl/graph/AbstractMatrixGraph.py", line 1287, in __getstate__
    self.save(tempFile.name)
  File "/usr/local/lib/python2.7/dist-packages/apgl/graph/AbstractMatrixGraph.py", line 558, in save
    import zipfile
  File "/usr/lib/python2.7/zipfile.py", line 464, in <module>
    class ZipExtFile(io.BufferedIOBase):
AttributeError: 'module' object has no attribute 'BufferedIOBase'

======================================================================
ERROR: testLoad (graph.test.DenseGraphTest.DenseGraphTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/apgl/graph/test/MatrixGraphTest.py", line 1619, in testLoad
    graph.save(tempFile)
  File "/usr/local/lib/python2.7/dist-packages/apgl/graph/AbstractMatrixGraph.py", line 558, in save
    import zipfile
  File "/usr/lib/python2.7/zipfile.py", line 464, in <module>
    class ZipExtFile(io.BufferedIOBase):
AttributeError: 'module' object has no attribute 'BufferedIOBase'

======================================================================
ERROR: testPickle (graph.test.DenseGraphTest.DenseGraphTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/apgl/graph/test/MatrixGraphTest.py", line 2309, in testPickle
    output = pickle.dumps(graph)
  File "/usr/lib/python2.7/pickle.py", line 1374, in dumps
    Pickler(file, protocol).dump(obj)
  File "/usr/lib/python2.7/pickle.py", line 224, in dump
    self.save(obj)
  File "/usr/lib/python2.7/pickle.py", line 306, in save
    rv = reduce(self.proto)
  File "/usr/lib/python2.7/copy_reg.py", line 84, in _reduce_ex
    dict = getstate()
  File "/usr/local/lib/python2.7/dist-packages/apgl/graph/AbstractMatrixGraph.py", line 1287, in __getstate__
    self.save(tempFile.name)
  File "/usr/local/lib/python2.7/dist-packages/apgl/graph/AbstractMatrixGraph.py", line 558, in save
    import zipfile
  File "/usr/lib/python2.7/zipfile.py", line 464, in <module>
    class ZipExtFile(io.BufferedIOBase):
AttributeError: 'module' object has no attribute 'BufferedIOBase'

----------------------------------------------------------------------
Ran 423 tests in 46.433s

FAILED (errors=4, skipped=120)

Answer 1

It seems to me you have some kind of an Ubuntu problem.

   File "/usr/lib/python2.7/zipfile.py", line 464, in <module>
   class ZipExtFile(io.BufferedIOBase):
AttributeError: 'module' object has no attribute 'BufferedIOBase'

Indicates that something is wrong with your python installation.

Did you install it your self?

Plus … while pip is great, you should prefer to work with you package manager, and only if you must install really new versions or non-packaged versions you should use pip. Hence instead of installing with pip do,

apt-get install python-scipy python-numpy python-matplotlib

And only then install apgl with pip.

I tested my installation apgl successfully on a Debian Wheezy with packages updated as of today (13-Sep-2012), and the test results are fine.

 In [22]: apgl.test()
Running tests from /usr/local/lib/python2.7/dist-packages/apgl
......./usr/lib/python2.7/dist-packages/scipy/sparse/compressed.py:486: SparseEfficiencyWarning: changing the sparsity structure of a csr_matrix is expensive. lil_matrix is more efficient.
  SparseEfficiencyWarning)
....s...........................................................................................ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss...................................................................................................................................................sssssssss...ssssssssssssssssssssssssssssssssssss......................s....s.........................ss
----------------------------------------------------------------------
Ran 423 tests in 25.454s

OK (skipped=120)